The interesting question with the internet is what is public and what isn't. For instance, the fact that the Green line's tracks join Amtrak's tracks at Riverside isn't publicized, but is known by a lot of people and easily observed.
Below is a blueprint of the Boylston Station (available through Wikipedia), which is where the south tunnel branched off from the rest of the Green line. It's the two tracks to the lower left. The outbound track crossed the other Green line tracks by an elevation separation.
Now I haven't been to Boylston in years. Nor do I know what the T's inactive fleet looks like these days. (According to Wikipedia it's approximately a 150 cars.) I was down there mainly during the Boeing fiasco, when the T was having to put a lot of the Boeings into storage, and bringing out the retired Pullman's.
A lot of these cars are (were) stored at Riverside, which is also where the Green line's main repair shop is located. However, at least in the past, the T had cars stored in all sorts of weird location, utilizing tracks that were no longer in use. These stored cars, even if used as scrap, have a substantial value, and the T police are concerned about vandalism problems. My guess is there now exists a very extensive video monitoring system.
If you go to Boylston station, especially armed with the blueprint, I think a lot of your questions will be answered. Also, if you travel between Park Street and Government Center, you'll see a lot of signs of the Scollay Square station and trackwork.
Best of luck,
Jim Clark-Dawe